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Zinc in PDB 8d4x: Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form

Enzymatic activity of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form

All present enzymatic activity of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form:
2.3.2.26;

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form (pdb code 8d4x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form, PDB code: 8d4x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8d4x

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Zinc binding site 1 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2801

b:63.8
occ:1.00
 SG A:CYS1232 2.3 86.2 1.0
SG A:CYS1179 2.3 59.1 1.0
SG A:CYS1208 2.3 69.9 1.0
SG A:CYS1211 2.3 76.0 1.0
CB A:CYS1211 3.4 63.1 1.0
CB A:CYS1232 3.4 72.5 1.0
CB A:CYS1179 3.7 57.8 1.0
CB A:CYS1208 3.8 58.9 1.0
N A:CYS1208 4.0 59.3 1.0
N A:SER1180 4.1 69.4 1.0
CA A:CYS1179 4.2 56.4 1.0
ZN A:ZN2802 4.3 97.3 1.0
N A:CYS1211 4.3 67.2 1.0
OG1 A:THR1242 4.4 52.9 1.0
CB A:CYS1234 4.4 89.0 1.0
CA A:CYS1211 4.4 64.3 1.0
CA A:CYS1208 4.5 55.3 1.0
C A:CYS1179 4.7 66.1 1.0
CA A:CYS1232 4.8 68.3 1.0
CB A:CYS1207 4.9 68.2 1.0
N A:PHE1181 4.9 48.6 1.0
C A:CYS1207 4.9 69.1 1.0
CA A:CYS1207 4.9 63.8 1.0
CB A:SER1180 4.9 56.7 1.0
SG A:CYS1240 5.0 58.1 1.0

Zinc binding site 2 out of 6 in 8d4x

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Zinc binding site 2 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2802

b:97.3
occ:1.00
 SG A:CYS1240 2.3 58.1 1.0
SG A:CYS1215 2.3 72.9 1.0
SG A:CYS1211 2.3 76.0 1.0
SG A:CYS1234 2.3 103.6 1.0
CB A:CYS1234 3.1 89.0 1.0
OG1 A:THR1242 3.4 52.9 1.0
CB A:CYS1215 3.4 52.0 1.0
CB A:CYS1211 3.5 63.1 1.0
CB A:CYS1240 3.6 55.1 1.0
CA A:CYS1240 3.9 54.8 1.0
CA A:CYS1211 4.2 64.3 1.0
ZN A:ZN2801 4.3 63.8 1.0
CA A:CYS1234 4.5 82.3 1.0
CB A:THR1242 4.6 42.4 1.0
N A:LYS1241 4.6 53.6 1.0
CG2 A:THR1242 4.7 47.7 1.0
C A:CYS1240 4.7 53.4 1.0
C A:CYS1234 4.8 85.0 1.0
CA A:CYS1215 4.8 45.8 1.0
N A:THR1242 4.8 41.8 1.0
N A:CYS1240 5.0 57.6 1.0

Zinc binding site 3 out of 6 in 8d4x

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Zinc binding site 3 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2803

b:74.8
occ:1.00
 ND1 A:HIS1216 2.0 47.8 1.0
ND1 A:HIS1219 2.0 49.4 1.0
SG A:CYS1196 2.3 78.8 1.0
SG A:CYS1199 2.3 76.0 1.0
CE1 A:HIS1216 2.8 54.4 1.0
CE1 A:HIS1219 2.9 52.6 1.0
CG A:HIS1219 3.0 46.3 1.0
CB A:CYS1199 3.1 66.9 1.0
CG A:HIS1216 3.2 47.5 1.0
CB A:HIS1219 3.4 47.5 1.0
N A:CYS1199 3.5 66.3 1.0
CB A:CYS1196 3.6 73.1 1.0
CB A:HIS1216 3.7 49.0 1.0
CA A:CYS1199 3.9 66.5 1.0
NE2 A:HIS1216 4.0 51.1 1.0
NE2 A:HIS1219 4.1 58.0 1.0
CD2 A:HIS1219 4.1 52.5 1.0
CD2 A:HIS1216 4.2 50.4 1.0
CA A:HIS1216 4.3 45.0 1.0
CB A:THR1198 4.3 65.8 1.0
CG2 A:THR1198 4.4 66.2 1.0
C A:THR1198 4.5 60.8 1.0
CA A:THR1198 4.8 62.8 1.0
CA A:HIS1219 5.0 41.7 1.0
N A:THR1198 5.0 64.2 1.0
CA A:CYS1196 5.0 70.5 1.0

Zinc binding site 4 out of 6 in 8d4x

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Zinc binding site 4 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2801

b:90.9
occ:1.00
 SG B:CYS1232 2.3 96.7 1.0
SG B:CYS1211 2.3 75.9 1.0
SG B:CYS1179 2.3 64.6 1.0
SG B:CYS1208 2.3 68.9 1.0
CB B:CYS1211 3.2 60.0 1.0
CB B:CYS1232 3.4 89.2 1.0
CB B:CYS1208 3.7 66.3 1.0
CB B:CYS1179 3.7 56.2 1.0
N B:CYS1208 3.8 61.7 1.0
N B:SER1180 4.0 72.9 1.0
CA B:CYS1179 4.2 55.3 1.0
CA B:CYS1211 4.2 56.1 1.0
N B:CYS1211 4.3 69.8 1.0
CA B:CYS1208 4.3 63.8 1.0
CB B:CYS1234 4.4 88.0 1.0
ZN B:ZN2802 4.4 128.7 1.0
C B:CYS1179 4.6 63.4 1.0
CA B:CYS1232 4.8 89.3 1.0
OG1 B:THR1242 4.8 54.5 1.0
C B:CYS1207 4.9 73.7 1.0
CB B:SER1180 4.9 69.1 1.0
CA B:CYS1207 4.9 77.4 1.0
CB B:CYS1207 4.9 77.1 1.0
N B:PHE1181 4.9 77.0 1.0
C B:CYS1208 5.0 67.6 1.0

Zinc binding site 5 out of 6 in 8d4x

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Zinc binding site 5 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2802

b:128.7
occ:1.00
 SG B:CYS1240 2.3 77.7 1.0
SG B:CYS1215 2.3 72.7 1.0
SG B:CYS1211 2.3 75.9 1.0
SG B:CYS1234 2.3 100.8 1.0
CB B:CYS1234 3.1 88.0 1.0
CB B:CYS1240 3.4 68.4 1.0
CB B:CYS1215 3.4 52.0 1.0
CB B:CYS1211 3.6 60.0 1.0
OG1 B:THR1242 3.8 54.5 1.0
CA B:CYS1240 3.9 64.0 1.0
CA B:CYS1211 4.2 56.1 1.0
ZN B:ZN2801 4.4 90.9 1.0
CA B:CYS1234 4.5 80.8 1.0
N B:LYS1241 4.6 61.0 1.0
C B:CYS1240 4.7 65.3 1.0
C B:CYS1234 4.8 84.3 1.0
CA B:CYS1215 4.8 44.9 1.0
CG2 B:THR1242 4.9 53.4 1.0
O B:CYS1211 4.9 64.7 1.0
CB B:THR1242 4.9 50.6 1.0
O B:LYS1239 4.9 75.4 1.0
C B:CYS1211 5.0 49.9 1.0

Zinc binding site 6 out of 6 in 8d4x

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Zinc binding site 6 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2803

b:86.1
occ:1.00
 ND1 B:HIS1216 2.0 47.2 1.0
ND1 B:HIS1219 2.0 58.1 1.0
SG B:CYS1199 2.3 81.5 1.0
SG B:CYS1196 2.3 97.9 1.0
CE1 B:HIS1216 2.5 50.9 1.0
CB B:CYS1199 2.7 73.8 1.0
CE1 B:HIS1219 3.0 60.0 1.0
CG B:HIS1219 3.0 50.9 1.0
CG B:HIS1216 3.3 45.2 1.0
CB B:HIS1219 3.4 50.8 1.0
N B:CYS1199 3.6 74.8 1.0
CB B:CYS1196 3.7 83.9 1.0
CA B:CYS1199 3.7 75.8 1.0
NE2 B:HIS1216 3.8 46.1 1.0
CB B:HIS1216 4.0 49.4 1.0
NE2 B:HIS1219 4.1 61.2 1.0
CD2 B:HIS1219 4.1 55.3 1.0
CD2 B:HIS1216 4.2 46.4 1.0
CA B:HIS1216 4.6 47.3 1.0
C B:THR1198 4.7 73.8 1.0
CA B:HIS1219 4.9 50.2 1.0
CB B:THR1198 5.0 74.5 1.0

Reference:

F.Wang, Q.He, W.Zhan, Z.Yu, E.Finkin-Groner, X.Ma, G.Lin, H.Li. Structure of the Human UBR5 E3 Ubiquitin Ligase Structure 2023.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2023.03.010
Page generated: Fri Aug 22 09:06:41 2025

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